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- PDB-3gaf: 2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 3gaf
Title2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase from Brucella Melitensis
Components7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BRUCELLA / MELITENSIS / HYDROXYSTEROID / DEHYDROGENASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / STRUCTURAL GENOMICS
Function / homology
Function and homology information


7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase (NAD+) activity / monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase from Brucella Melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 22, 2025Group: Database references / Structure summary
Category: audit_author / citation_author / pdbx_entry_details
Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
B: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
C: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
D: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
E: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
F: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
G: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
H: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)210,7138
Polymers210,7138
Non-polymers00
Water6,612367
1
A: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
F: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
G: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
H: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)105,3564
Polymers105,3564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-116 kcal/mol
Surface area33490 Å2
MethodPISA
2
B: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
C: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
D: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE
E: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)105,3564
Polymers105,3564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-117 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.320, 134.777, 105.269
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Mass: 26339.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: BMEI0406 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4
Details: 20% PEG 1500, 0.1M MIB buffer/salt, pH 4.0, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: SATURN 944 / Detector: CCD / Date: Jan 1, 2008 / Details: MULTI-LAYER OPTICS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 99242 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.188
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.2-2.283.20.58993.4
2.28-2.373.60.47798.2
2.37-2.4840.38199.9
2.48-2.614.20.301100
2.61-2.774.30.221100
2.77-2.994.30.147100
2.99-3.294.30.103100
3.29-3.764.30.067100
3.76-4.744.20.055100
4.74-504.20.03399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.97 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.87 Å
Translation2.5 Å48.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AHI

1ahi


Resolution: 2.2→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.517 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24425 4955 5 %RANDOM
Rwork0.19623 ---
obs0.19862 94203 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.03 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13764 0 0 367 14131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213990
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.94619008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92951941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53624.447506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.368152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1391568
X-RAY DIFFRACTIONr_chiral_restr0.0880.22226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.26294
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.29615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2587
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.2210
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.59878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.234215094
X-RAY DIFFRACTIONr_scbond_it1.7634613
X-RAY DIFFRACTIONr_scangle_it2.7754.53914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 298 -
Rwork0.283 6459 -
obs--92.07 %

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